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	   <h2>flyted-service.js</h2>
	
</center>

	


<h4>Summary</h4>
<p>
	
		This script defines utilities for interacting with data from www.fly-ted.org.
 <BR/><BR/><B>Version: </B>$Revision:538 $ on $Date: 2008-08-27 09:08:41 +0100 (Wed, 27 Aug 2008) $ by $Author: aliman $
 <BR/><BR/><B>Requires:</B><UL>- YAHOO.util.Connect<BR/>- flyui.flyted.GeneNameMappings
 TODO license terms</UL><B>Author:</B> <a href="http://purl.org/net/aliman">Alistair Miles</a>, Graham Klyne, Jun Zhao
 <BR/>
	
</p>

<hr>


    <table border="1" cellpadding="3" cellspacing="0" width="100%">
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    <td colspan=2><font size="+2">
    
        <b>Class Summary</b>
    
    </font></td>
    </tr>
    
    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyted/ImagePool.html">flyui.flyted.ImagePool</a></b></td>
    <td>&nbsp;</td>
    </tr>
    
    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyted/ProbePool.html">flyui.flyted.ProbePool</a></b></td>
    <td>&nbsp;</td>
    </tr>
    
    <tr bgcolor="white" class="TableRowColor">
    <td width="15%"><b><a href="flyui/flyted/Service.html">flyui.flyted.Service</a></b></td>
    <td>&nbsp;</td>
    </tr>
    
    </table>
    <hr/> 


<!-- ========== METHOD SUMMARY =========== -->

<!-- ========== END METHOD SUMMARY =========== -->


        <pre class="sourceview"><span class="comment">/**
 * <span class="attrib">@fileoverview</span>
 * This script defines utilities for interacting with data from www.fly-ted.org.
 * <span class="attrib">@author</span> &lt;a href="http://purl.org/net/aliman"&gt;Alistair Miles&lt;/a&gt;, Graham Klyne, Jun Zhao
 * <span class="attrib">@version</span> $Revision:538 $ on $Date: 2008-08-27 09:08:41 +0100 (Wed, 27 Aug 2008) $ by $Author: aliman $
 * <span class="attrib">@requires</span> YAHOO.util.Connect
 * <span class="attrib">@requires</span> flyui.flyted.GeneNameMappings
 * TODO license terms
 */</span>

<span class="comment">// create a namespace if not already defined</span>
flyui.namespace(<span class="literal">"flyui.flyted"</span>);


<span class="comment">/**
 * TODO doc me
 */</span>
flyui.flyted.Service = <span class="reserved">function</span> (endpointURL) {
	<span class="comment">/**
	 * <span class="attrib">@private</span>
	 */</span>
	<span class="reserved">this</span>._endpointURL = endpointURL;
}


<span class="comment">/**
 * TODO doc me
 */</span>
flyui.flyted.Service.<span class="reserved">prototype</span>.query = <span class="reserved">function</span> (query, success, failure){
	log(<span class="literal">"flyui.flyted.Service :: query request: "</span>+query);
	
	<span class="comment">// define the callback object</span>
	var callback = {
		success: success,
		failure: failure
	};
			
	var url = <span class="reserved">this</span>._buildURL(query);
	
	log(<span class="literal">"flyui.flyted.Service :: make the request to "</span>+url);
	var request = YAHOO.util.Connect.asyncRequest(<span class="literal">"GET"</span>, url, callback, null);
	
};


<span class="comment">/**
 * TODO doc me
 */</span>
flyui.flyted.Service.<span class="reserved">prototype</span>.findImagesByFlytedProbeName = <span class="reserved">function</span>( probeName, success, failure ) {
	log(<span class="literal">"flyui.flyted.Service :: findImagesByFlytedProbeName: "</span>+probeName);
	
	var successAdapter = flyui.flyted.Service._buildSuccessAdapterForFindImagesByFlytedProbeName(success);

	var query = flyui.flyted.Service._buildQueryForFindImagesByFlytedProbeName(probeName);
	
	<span class="reserved">this</span>.query(query, successAdapter, failure);
	
};


<span class="comment">/**
 * Find images in the FlyTED database for the given flybase gene ID.
 * <span class="attrib">@param</span> {String} flybaseGeneID the flybase gene ID e.g. FBgn012345
 * <span class="attrib">@param</span> {Function} success the success case callback function, which must accept an array of 
 * flyui.flyted.Image objects
 * <span class="attrib">@param</span> {Function} failure the failure case callback function, which must accept a YUI HTTP response object
 */</span>
flyui.flyted.Service.<span class="reserved">prototype</span>.findImagesByFlybaseGeneID = <span class="reserved">function</span>( flybaseGeneID, success, failure) {
	log(<span class="literal">"flyui.flyted.Service :: findImagesByFlybaseGeneID: "</span>+flybaseGeneID);
	
	var successAdapter = flyui.flyted.Service._buildSuccessAdapterForFindImagesByFlybaseGeneID(success);

	var query = flyui.flyted.Service._buildQueryForFindImagesByFlybaseGeneID(flybaseGeneID);
	
	<span class="reserved">this</span>.query(query, successAdapter, failure);
	
}

<span class="comment">/**
 * Return a success case request handler for the findImagesByFlytedProbeName method.
 * <span class="attrib">@param</span> {Function} adaptedSuccess the function to call with an array of Image objects
 * <span class="attrib">@return</span> a success callback to use in the HTTP request
 * <span class="attrib">@type</span> Function
 * <span class="attrib">@private</span>
 * <span class="attrib">@static</span>
 */</span>
flyui.flyted.Service._buildSuccessAdapterForFindImagesByFlybaseGeneID = <span class="reserved">function</span>( adaptedSuccess ) {

	<span class="reserved">return</span> <span class="reserved">function</span>(responseObject) {
		
		log(<span class="literal">"response received: "</span>+responseObject.status, <span class="literal">"debug"</span>);
		
		<span class="comment">// try parsing response text as json</span>
		log(<span class="literal">"parsing response: "</span>+responseObject.responseText, <span class="literal">"debug"</span>);
		var resultSet = YAHOO.lang.JSON.parse(responseObject.responseText);
		
		<span class="comment">// convert result set to an array of genes</span>
		var images = flyui.flyted.Image.newInstancesFromSPARQLResults(resultSet);
		
		<span class="comment">// complete the request</span>
		adaptedSuccess(images);
	}

};


<span class="comment">/**
 * Return a success case request handler for the findImagesByFlytedProbeName method.
 * <span class="attrib">@param</span> {Function} adaptedSuccess the function to call with an array of Image objects
 * <span class="attrib">@return</span> a success callback to use in the HTTP request
 * <span class="attrib">@type</span> Function
 * <span class="attrib">@private</span>
 * <span class="attrib">@static</span>
 */</span>
flyui.flyted.Service._buildSuccessAdapterForFindImagesByFlytedProbeName = <span class="reserved">function</span>( adaptedSuccess ) {

	<span class="reserved">return</span> <span class="reserved">function</span>(responseObject) {
		
		log(<span class="literal">"response received: "</span>+responseObject.status, <span class="literal">"debug"</span>);
		
		<span class="comment">// try parsing response text as json</span>
		log(<span class="literal">"parsing response: "</span>+responseObject.responseText, <span class="literal">"debug"</span>);
		var resultSet = YAHOO.lang.JSON.parse(responseObject.responseText);
		
		<span class="comment">// convert result set to an array of genes</span>
		var images = flyui.flyted.Image.newInstancesFromSPARQLResults(resultSet);
		
		<span class="comment">// complete the request</span>
		adaptedSuccess(images);
	}

};


<span class="comment">/**
 * Build a SPARQL query to retrieve images by flyted probe name.
 * <span class="attrib">@param</span> {String} anyName the probe name to search by
 * <span class="attrib">@return</span> a SPARQL query
 * <span class="attrib">@type</span> String
 * <span class="attrib">@private</span>
 * <span class="attrib">@static</span>
 */</span>
flyui.flyted.Service._buildQueryForFindImagesByFlytedProbeName = <span class="reserved">function</span>( probeName ) {

	var prefixes = 	<span class="literal">"PREFIX flyted: &lt;http://purl.org/net/flyted/schema/&gt; "</span> +
					<span class="literal">"PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; "</span> +
					<span class="literal">"PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; "</span>;
					
	var body = 		<span class="literal">"SELECT DISTINCT *  WHERE { "</span> +
						<span class="literal">"?fullImageURL "</span> +
							<span class="literal">"flyted:probe ?probe ; "</span> +
							<span class="comment">//"flyted:associatesToGene ?gene ; " +</span>
							<span class="literal">"flyted:thumbnail ?thumbnailURL; "</span> +
							<span class="literal">"rdfs:seeAlso ?flytedURL; "</span> +
							<span class="literal">"rdfs:label ?caption ."</span> +
						<span class="literal">"?probe rdfs:label '"</span> + probeName + <span class="literal">"' ."</span> +
					<span class="literal">"}"</span>;
						
	var query = prefixes + body;

	<span class="reserved">return</span> query;
};

flyui.flyted.Service._buildQueryForFindImagesByFlybaseGeneID = <span class="reserved">function</span>( flybaseGeneID ) {
	var prefixes = 	<span class="literal">"PREFIX flyted: &lt;http://purl.org/net/flyted/schema/&gt; "</span> +
					<span class="literal">"PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; "</span> +
					<span class="literal">"PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; "</span>;
					<span class="literal">"PREFIX so: &lt;http://purl.org/obo/owl/SO#&gt; "</span>;
					
	var body = 		<span class="literal">"SELECT DISTINCT ?fullImageURL ?thumbnailURL ?flytedURL ?caption ?probe ?probeLabel WHERE { "</span> +
						<span class="literal">"?probe flyted:hybridisesTranscriptOf &lt;http://openflydata.org/id/flybase/feature/"</span> + flybaseGeneID + <span class="literal">"&gt; ;"</span> +
							<span class="literal">"rdfs:label ?probeLabel ."</span> +
						<span class="literal">"?fullImageURL "</span> +
							<span class="literal">"flyted:probe ?probe ; "</span> +
							<span class="literal">"flyted:thumbnail ?thumbnailURL; "</span> +
							<span class="literal">"rdfs:seeAlso ?flytedURL; "</span> +
							<span class="literal">"rdfs:label ?caption ."</span> +
					<span class="literal">"}"</span>;
						
	var query = prefixes + body;

	<span class="reserved">return</span> query;
	
};


<span class="comment">/**
 * Build a SPARQL query to retrieve images by a union of multiple flyted probe names.
 * <span class="attrib">@param</span> {[String]} anyNames the array of probe names to search by
 * <span class="attrib">@return</span> a SPARQL query
 * <span class="attrib">@type</span> String
 * <span class="attrib">@private</span>
 * <span class="attrib">@static</span>
 */</span>
<span class="comment">//flyui.flyted.Service._buildQueryForFindImagesByUnionOfFlytedProbeNames = function( probeNames ) {</span>
<span class="comment">//</span>
<span class="comment">//	var prefixes = 	"PREFIX flyted: &lt;http://purl.org/net/flyted/schema/&gt; " +</span>
<span class="comment">//					"PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; " +</span>
<span class="comment">//					"PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; ";</span>
<span class="comment">//		</span>
<span class="comment">//	if (probeNames.length == 0) {</span>
<span class="comment">//		// this should never happen	</span>
<span class="comment">//		throw {name:"flyui.flyted.Service.InvalidQueryException", message:"cannot query for union of empty array of probe names"};</span>
<span class="comment">//	}				</span>
<span class="comment">//	else if (probeNames.length == 1) {</span>
<span class="comment">//		return flyui.flyted.Service._buildQueryForFindImagesByFlytedProbeName(probeNames[0]);</span>
<span class="comment">//	}</span>
<span class="comment">//	else {</span>
<span class="comment">//		</span>
<span class="comment">//		var pattern = function( probeName ) {</span>
<span class="comment">//			return 	"{ "+</span>
<span class="comment">//						"?fullImageURL " +</span>
<span class="comment">//							"flyted:probe ?probe ; " +</span>
<span class="comment">//							//"flyted:associatesToGene ?gene ; " +</span>
<span class="comment">//							"flyted:thumbnail ?thumbnailURL; " +</span>
<span class="comment">//							"rdfs:seeAlso ?flytedURL; " +</span>
<span class="comment">//							"rdfs:label ?caption ." +</span>
<span class="comment">//						"?probe rdfs:label '" + probeName + "' ." +</span>
<span class="comment">//					"} ";</span>
<span class="comment">//		}</span>
<span class="comment">//		</span>
<span class="comment">//		var body = 		"SELECT DISTINCT * WHERE { ";</span>
<span class="comment">//		body +=			pattern(probeNames[0]);</span>
<span class="comment">//		for (var i=1; i&lt;probeNames.length; i++) {</span>
<span class="comment">//			body += 	"UNION ";</span>
<span class="comment">//			body +=		pattern(probeNames[i]);</span>
<span class="comment">//		}</span>
<span class="comment">//		body += 		"}";</span>
<span class="comment">//		</span>
<span class="comment">//	}</span>
<span class="comment">//</span>
<span class="comment">//	var query = prefixes + body;</span>
<span class="comment">//</span>
<span class="comment">//	return query;</span>
<span class="comment">//}</span>


<span class="comment">/**
 * Construct the request URL for the given SPARQL query.
 * <span class="attrib">@private</span>
 * <span class="attrib">@param</span> {String} query a SPARQL query
 * <span class="attrib">@return</span> a request URL
 * <span class="attrib">@type</span> String
 */</span>
flyui.flyted.Service.<span class="reserved">prototype</span>._buildURL = <span class="reserved">function</span>( query ) {
	<span class="reserved">return</span> <span class="reserved">this</span>._endpointURL + <span class="literal">"?output=json&amp;query="</span> + escape(query);
};


<span class="comment">/**
 * Map a string to a list of strings via a supplied mapping table,
 * returnimng an empty list if the supplied key is not present. 
 * <span class="attrib">@param</span> {String} key 		a key value to be mapped
 * <span class="attrib">@param</span> {Object} table 	an object with members that are arrays of strings
 * <span class="attrib">@return</span> an array of string values, which may be empty if the given key is not found
 * <span class="attrib">@type</span> [String]
 */</span>
flyui.flyted.Service.mapNameUsingTable = <span class="reserved">function</span> ( key, table ) {
	var result = table[key];
	<span class="reserved">if</span> (typeof result == <span class="literal">"undefined"</span> || !result ) {
		result = [];
	}
	<span class="reserved">return</span> result;
}


<span class="comment">/**
 * Map a Flybase ID to zero, one or more FlyTED gene names.  Note that if there is no known mapping
 * for the supplied gene name, an empty (zero-length) array is returned.
 * <span class="attrib">@param</span> {String} a Flybase ID
 * <span class="attrib">@return</span> an array of FlyTED gene names that return data corresponding to the given Flybase ID
 * <span class="attrib">@type</span> [String]
 */</span>
<span class="comment">//flyui.flyted.Service.mapFlybaseIDToFlytedGeneName = function( flybaseID ) {</span>
<span class="comment">//	</span>
<span class="comment">//	return flyui.flyted.Service.mapNameUsingTable(flybaseID, flyui.flyted.GeneNameMappings.flybaseToFlyted);</span>
<span class="comment">//	</span>
<span class="comment">//}</span>
<span class="comment">//</span>
<span class="comment">//</span>
<span class="comment">///**</span>
<span class="comment">// * Map a Flybase ID to zero, one or more FlyTED gene names.  Note that if there is no known mapping</span>
<span class="comment">// * for the supplied Flybase ID, an empty (zero-length) array is returned.</span>
<span class="comment">// * <span class="attrib">@param</span> {String} a Flybase ID</span>
<span class="comment">// * <span class="attrib">@return</span> an array of FlyTED gene names that return data corresponding to the given Flybase ID</span>
<span class="comment">// * <span class="attrib">@type</span> [String]</span>
<span class="comment">// */</span>
<span class="comment">//flyui.flyted.Service.mapFlytedGeneNameToFlybaseID = function( flytedName ) {</span>
<span class="comment">//</span>
<span class="comment">//	return flyui.flyted.Service.mapNameUsingTable(flytedName, flyui.flyted.GeneNameMappings.flytedToFlybase);</span>
<span class="comment">//</span>
<span class="comment">//}</span>


<span class="comment">/**
 * TDO doc me
 */</span>
flyui.flyted.Image = <span class="reserved">function</span> () {
	
	<span class="comment">/**
	 * <span class="attrib">@type</span> String
	 */</span>
	<span class="reserved">this</span>.fullImageURL = null;
	
	<span class="comment">/**
	 * <span class="attrib">@type</span> String
	 */</span>
	<span class="reserved">this</span>.thumbnailURL = null;
	
	<span class="comment">/**
	 * <span class="attrib">@type</span> String
	 */</span>
	 
	<span class="reserved">this</span>.flytedURL = null;
	
	<span class="comment">/**
	 * <span class="attrib">@type</span> String
	 */</span>
	<span class="reserved">this</span>.caption = null;
	
	<span class="comment">/**
	 * <span class="attrib">@type</span> String
	 */</span>
	<span class="reserved">this</span>.probe = null;
	
<span class="comment">//	this.addProbe = function (probe){</span>
<span class="comment">//		flyui.util.appendIfNotMember(that.images, image);</span>
<span class="comment">//	};</span>
	
}


<span class="comment">/**
 * TODO doc me
 */</span>
flyui.flyted.Image.newInstancesFromSPARQLResults = <span class="reserved">function</span>(resultSet){
	var bindings = resultSet.results.bindings;
	var imagePool = new flyui.flyted.ImagePool();
	var probePool = new flyui.flyted.ProbePool();
	
	<span class="reserved">for</span> (var i=0; i&lt;bindings.length; i++) {
		var binding = bindings[i];
		
		var imageURI = binding.fullImageURL.value;
		<span class="comment">//TODO</span>
		var image = imagePool.get(imageURI);
		image.fullImageURL = binding.fullImageURL.value;
		image.thumbnailURL = binding.thumbnailURL.value;
		image.flytedURL = binding.flytedURL.value;
		image.caption = binding.caption.value;
		
		<span class="reserved">if</span> (binding.probe){
			var probeURI = binding.probe.value;
			var probe = probePool.get(probeURI);
			
			<span class="reserved">if</span> (!probe.probeLabels){
				probe.probeLabels = new Array();
			}

			<span class="reserved">if</span> (binding.probeLabel) {
				var probeLabel = binding.probeLabel.value;
				flyui.util.appendIfNotMember(probe.probeLabels, probeLabel);
			}
			<span class="comment">//image.addProbe(probe);</span>
			image.probe = probe;
		}		
	}
	
	<span class="reserved">return</span> imagePool.toArray();
}

flyui.flyted.ImagePool = <span class="reserved">function</span>() {
	<span class="comment">/**
	 * <span class="attrib">@private</span>
	 */</span>
	<span class="reserved">this</span>._pool = new Object();
};

flyui.flyted.ImagePool.<span class="reserved">prototype</span>.toArray = <span class="reserved">function</span>() {
	var array = new Array();
	<span class="reserved">for</span> (var key in <span class="reserved">this</span>._pool) {
		array[array.length] = <span class="reserved">this</span>._pool[key];
	}
	<span class="reserved">return</span> array;
}

flyui.flyted.ImagePool.<span class="reserved">prototype</span>.get = <span class="reserved">function</span>( imagepath ) {
	
	var image = <span class="reserved">this</span>._pool[imagepath];
	
	<span class="reserved">if</span> ( typeof image == <span class="literal">"undefined"</span> || !image ) {
		image = new flyui.flyted.Image();		
		<span class="reserved">this</span>._pool[imagepath] = image;	
	}
	
	<span class="reserved">return</span> image;

};

flyui.flyted.ProbePool = <span class="reserved">function</span>() {
	<span class="comment">/**
	 * <span class="attrib">@private</span>
	 */</span>
	<span class="reserved">this</span>._pool = new Object();
};

flyui.flyted.ProbePool.<span class="reserved">prototype</span>.get = <span class="reserved">function</span>( probeURI ) {
	
	var probe = <span class="reserved">this</span>._pool[probeURI];
	
	<span class="reserved">if</span> (!probe ) {
		probe = new Object();
		probe.probeURI = probeURI;
		<span class="reserved">this</span>._pool[probeURI] = probe;	
	}
	
	<span class="reserved">return</span> probe;

};

flyui.flyted.ProbePool.<span class="reserved">prototype</span>.toArray = <span class="reserved">function</span>() {
	var array = new Array();
	<span class="reserved">for</span> (var key in <span class="reserved">this</span>._pool) {
		array[array.length] = <span class="reserved">this</span>._pool[key];
	}
	<span class="reserved">return</span> array;
}</pre>
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<div class="jsdoc_ctime">Documentation generated by <a href="http://jsdoc.sourceforge.net/" target="_parent">JSDoc</a> on Fri Dec  5 17:34:11 2008</div>
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